Have a new metal roof that I am replaceing

have a 1996 pre-manufactured home had a manufactured rolled roof when it was built. That's where they take big roll of metal then stretch across roof one side to the other attaching both ends on each side. That was in 1996
Now 2018 I have gone over the top of that with new 29 gage roof panels with exposed fasteners. Witch first installed with 1" x 4" battens on 16" center were ran length of home nailed into each rafter that was on 24" centers. Now because of some low spots between the eave and the ridge. it looks wavey not straight or flat. I am removing this new 29 gage roof. and try again! Am replacing for other reasons. but want to make sure it is done right this time Don't really want to have to replace it a third time lol. Let me know if this should solve the problem?
before I install the panels use strings to shim under low spots in the 1" x 4" battens this should fix the waviness once the panels are reinstalled? This should have been done the first time? Let me know if anyone else has ever had this problem and what they did to solve this problem? Thank you in advance Johnny H.